In the Intel® Quartus® Prime Pro Edition software version 21.1 and prior, there is an issue with the Agilex SDM QSPI controller being disabled for the HPS after the initial FPGA configuration occurs during HPS boot first mode. This occurs after the first FPGA configuration from both U-Boot and/or Linux.
To work around this problem, you can re-probe the QSPI flash driver after the initial FPGA configuration.
To re-probe in U-Boot run this commmand:
SOCFPGA_AGILEX # sf probe
This problem is scheduled to be fixed in a future release of Intel® Quartus® Prime Pro Edition software.